How to organize bookmarks in the file browser?
You must edit a file called bookmarks.txt with your favorite text editor (e.g. notepad).
This file appears on your configuration folder of blender, which varies in location depending on your OS. As bookmarks are user specific, it will be in the user configuration path for your operating system. See the wiki.
Windows:
For Windows it is usually in %appdata%\Blender Foundation\Blender\2.69\config where 2.69 is the version of blender which you are using, and %appdata% is the AppData directory of your user folder).
Linux:
It will be in ~/.config/blender/2.69/config/, where ~ is your home directory.
OSX:
According to the wiki page about file paths, it should be in /Users/{user}/Library/Application Support/Blender/2.69/config/
Portable:
If you create a directory called config inside the 2.69 directory (where 2.69 is your version) this file will appear there the next time you run blender and add a bookmark.